Scripting in Fiji (Fiji Is Just ImageJ)

Abstract

Through the use of plugins, ImageJ is a very powerful image processing suite. Sometimes, however, it is desirable to control ImageJ and its plugins using a scripting language, to benefit from the full power of the Java API, but without the hassle to write a full-blown Java plugin.

Fiji – a distribution of ImageJ with a lot of plugins – bundles several scripting languages: Jython, JRuby, BeanShell, Javascript, and Clojure.

Fiji also comes with a script editor to develop and run the scripts in any of these languages conveniently (e.g. offering syntax-highlighting, easy lookup of the API documentation, etc).